Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1

Abstract

Background: Syntaxin-binding protein 1, encoded by STXBP1, is highly expressed in the brain and involved in fusing synaptic vesicles with the plasma membrane. Studies have shown that pathogenic loss-of-function variants in this gene result in various types of epilepsies, mostly beginning early in life. We were interested to model pathogenic missense variants on the protein structure to investigate the mechanism of pathogenicity and genotype-phenotype correlations.

Methods: We report 11 patients with pathogenic de novo mutations in STXBP1 identified in the first 4293 trios of the Deciphering Developmental Disorder (DDD) study, including six missense variants. We analyzed the structural locations of the pathogenic missense variants from this study and the literature, as well as population missense variants extracted from Exome Aggregation Consortium (ExAC).

Results: Pathogenic variants are significantly more likely to occur at highly conserved locations than population variants, and be buried inside the protein domain. Pathogenic mutations are also more likely to destabilize the domain structure compared with population variants, increasing the proportion of (partially) unfolded domains that are prone to aggregation or degradation. We were unable to detect any genotype-phenotype correlation, but unlike previously reported cases, most of the DDD patients with STXBP1 pathogenic variants did not present with very early-onset or severe epilepsy and encephalopathy, though all have developmental delay with intellectual disability and most display behavioral problems and suffered seizures in later childhood.

Conclusion: Variants across STXBP1 that cause loss of function can result in severe intellectual disability with or without seizures, consistent with a haploinsufficiency mechanism. Pathogenic missense mutations act through destabilization of the protein domain, making it prone to aggregation or degradation. The presence or absence of early seizures may reflect ascertainment bias in the literature as well as the broad recruitment strategy of the DDD study.

Keywords: Epilepsy; Exome Aggregation Consortium; Munc18; genomics; protein structure; syntaxin‐binding protein 1.

Figure 1

Cartoon representation of the role of STXBP1 in priming vesicle fusion, showing binding to syntaxin‐1 (closed conformation) and other members of the SNARE complex.

Figure 2

Domain architecture of syntaxin‐binding protein 1. The distribution of the population missense variants from ExAC are shown as a density plot on top (black) and is based on 65 unique missense variants; the bottom distribution shows all pathogenic variants from this study and the literature (magenta), and is based on 40 unique missense variants.

Figure 3

Ribbon diagram of syntaxin‐binding protein 1 (transparent, colored by domain as in Figure 1) in complex with part of syntaxin‐1 (red) with the Cα positions of pathogenic missense variants (magenta) and population missense variants (gray). The N‐peptide is shown in the cylinder representation (bottom left).

Figure 4

Boxplots of (A) residue accessiblity (Hubbard and Thornton 1993), (B) sequence conservation (Dodge et al. 1998; Ashkenazy et al. 2010), (C) number of interacting amino acids within the STXBP1 domain or (D) with syntaxin‐1, and (E) predicted change in stability of the protein domain (Schymkowitz et al. 2005) for pathogenic (pink) and population (gray) missense variants.

Figure 5

Structure of syntaxin‐binding protein 1 with the positions of the five missense pathogenic variants from the DDD study and their structural surroundings shown as insets.